Coarse-grained simulation of cellulose Iβ with application to long fibrils

Fan, Bingxin; Maranas, Janna K.

doi:10.1007/s10570-014-0481-2

Coarse-grained simulation of cellulose Iβ with application to long fibrils

Journal Article · Thu Oct 30 00:00:00 EDT 2014 · Cellulose

DOI:https://doi.org/10.1007/s10570-014-0481-2· OSTI ID:1385102

Fan, Bingxin; Maranas, Janna K.

Research Organization:: Energy Frontier Research Centers (EFRC) (United States). Center for Lignocellulose Structure and Formation (CLSF)

Sponsoring Organization:: USDOE SC Office of Basic Energy Sciences (SC-22)

DOE Contract Number:: SC0001090

OSTI ID:: 1385102

Journal Information:: Cellulose, Journal Name: Cellulose Journal Issue: 1 Vol. 22; ISSN 0969-0239

Publisher:: Springer

Country of Publication:: United States

Language:: English

References (63)

Why are coarse-grained force fields too fast? A look at dynamics of four coarse-grained polymers Depa, Praveen; Chen, Chunxia; Maranas, Janna K. The Journal of Chemical Physics, Vol. 134, Issue 1 https://doi.org/10.1063/1.3513365	journal	January 2011
Molecular Dynamics Simulations of Bulk Native Crystalline and Amorphous Structures of Cellulose Mazeau, K.; Heux, L. The Journal of Physical Chemistry B, Vol. 107, Issue 10 https://doi.org/10.1021/jp0219395	journal	March 2003
Native Cellulose: A Composite of Two Distinct Crystalline Forms Atalla, R. H.; Vanderhart, D. L. Science, Vol. 223, Issue 4633 https://doi.org/10.1126/science.223.4633.283	journal	January 1984
Coarse-grained simulations of lipid bilayers Stevens, Mark J. The Journal of Chemical Physics, Vol. 121, Issue 23 https://doi.org/10.1063/1.1814058	journal	December 2004
An improved OPLS-AA force field for carbohydrates Kony, D.; Damm, W.; Stoll, S. Journal of Computational Chemistry, Vol. 23, Issue 15 https://doi.org/10.1002/jcc.10139	journal	October 2002
The Hydrogen Bond in the Solid State Steiner, Thomas Angewandte Chemie International Edition, Vol. 41, Issue 1 https://doi.org/10.1002/1521-3773(20020104)41:1<48::AID-ANIE48>3.0.CO;2-U	journal	January 2002
Martini Coarse-Grained Force Field: Extension to Carbohydrates López, Cesar A.; Rzepiela, Andrzej J.; de Vries, Alex H. Journal of Chemical Theory and Computation, Vol. 5, Issue 12 https://doi.org/10.1021/ct900313w	journal	October 2009
Simulations of Phospholipids Using a Coarse Grain Model Shelley, John C.; Shelley, Mee Y.; Reeder, Robert C. The Journal of Physical Chemistry B, Vol. 105, Issue 40 https://doi.org/10.1021/jp011637n	journal	October 2001
Flow properties of microcrystalline cellulose suspension prepared by acid treatment of native cellulose Araki, Jun; Wada, Masahisa; Kuga, Shigenori Colloids and Surfaces A: Physicochemical and Engineering Aspects, Vol. 142, Issue 1 https://doi.org/10.1016/S0927-7757(98)00404-X	journal	November 1998
Dynamics of Cellulose−Water Interfaces: NMR Spin−Lattice Relaxation Times Calculated from Atomistic Computer Simulations Bergenstråhle, Malin; Wohlert, Jakob; Larsson, Per Tomas The Journal of Physical Chemistry B, Vol. 112, Issue 9 https://doi.org/10.1021/jp074641t	journal	March 2008
Crystal Structure and Hydrogen-Bonding System in Cellulose Iβ from Synchrotron X-ray and Neutron Fiber Diffraction Nishiyama, Yoshiharu; Langan, Paul; Chanzy, Henri Journal of the American Chemical Society, Vol. 124, Issue 31 https://doi.org/10.1021/ja0257319	journal	August 2002
Microfibril diameter in celery collenchyma cellulose: X-ray scattering and NMR evidence Kennedy, Craig J.; Cameron, Graeme J.; Šturcová, Adriana Cellulose, Vol. 14, Issue 3 https://doi.org/10.1007/s10570-007-9116-1	journal	March 2007
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations Brooks, Bernard R.; Bruccoleri, Robert E.; Olafson, Barry D. Journal of Computational Chemistry, Vol. 4, Issue 2 https://doi.org/10.1002/jcc.540040211	journal	July 1983
High-Temperature Behavior of Cellulose I Matthews, James F.; Bergenstråhle, Malin; Beckham, Gregg T. The Journal of Physical Chemistry B, Vol. 115, Issue 10 https://doi.org/10.1021/jp1106839	journal	March 2011
REACH Coarse-Grained Simulation of a Cellulose Fiber Glass, Dennis C.; Moritsugu, Kei; Cheng, Xiaolin Biomacromolecules, Vol. 13, Issue 9 https://doi.org/10.1021/bm300460f	journal	August 2012
Extraction of cellulose and preparation of nanocellulose from sisal fibers Morán, Juan I.; Alvarez, Vera A.; Cyras, Viviana P. Cellulose, Vol. 15, Issue 1 https://doi.org/10.1007/s10570-007-9145-9	journal	August 2007
Cellulose Microfibril Twist, Mechanics, and Implication for Cellulose Biosynthesis Zhao, Zhen; Shklyaev, Oleg E.; Nili, Abdolmajid The Journal of Physical Chemistry A, Vol. 117, Issue 12 https://doi.org/10.1021/jp3089929	journal	March 2013
Coarse Grained Model for Semiquantitative Lipid Simulations Marrink, Siewert J.; de Vries, Alex H.; Mark, Alan E. The Journal of Physical Chemistry B, Vol. 108, Issue 2 https://doi.org/10.1021/jp036508g	journal	January 2004
M3B: A Coarse Grain Force Field for Molecular Simulations of Malto-Oligosaccharides and Their Water Mixtures Molinero, Valeria; Goddard, William A. The Journal of Physical Chemistry B, Vol. 108, Issue 4 https://doi.org/10.1021/jp0354752	journal	January 2004
Cellulose: the structure slowly unravels O'Sullivan, Antoinette C. Cellulose, Vol. 4, Issue 3, p. 173-207 https://doi.org/10.1023/A:1018431705579	journal	January 1997
Cellulose Intercrystalline Structure Nickerson, R. F.; Habrle, J. A. Industrial & Engineering Chemistry, Vol. 39, Issue 11 https://doi.org/10.1021/ie50455a024	journal	November 1947
Exploring the utility of coarse-grained water models for computational studies of interfacial systems He, Xibing; Shinoda, Wataru; DeVane, Russell Molecular Physics, Vol. 108, Issue 15 https://doi.org/10.1080/00268976.2010.503197	journal	August 2010
Systematic Coarse Graining of Biomolecular and Soft-Matter Systems Ayton, Gary S.; Noid, Will G.; Voth, Gregory A. MRS Bulletin, Vol. 32, Issue 11 https://doi.org/10.1557/mrs2007.190	journal	November 2007
Coarse-grained molecular dynamics simulations of membrane proteins and peptides Bond, Peter J.; Holyoake, John; Ivetac, Anthony Journal of Structural Biology, Vol. 157, Issue 3 https://doi.org/10.1016/j.jsb.2006.10.004	journal	March 2007
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes Ryckaert, Jean-Paul; Ciccotti, Giovanni; Berendsen, Herman J. C. Journal of Computational Physics, Vol. 23, Issue 3 https://doi.org/10.1016/0021-9991(77)90098-5	journal	March 1977
A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils Srinivas, Goundla; Cheng, Xiaolin; Smith, Jeremy C. Journal of Chemical Theory and Computation, Vol. 7, Issue 8 https://doi.org/10.1021/ct200181t	journal	July 2011
Fast Parallel Algorithms for Short-Range Molecular Dynamics Plimpton, Steve Journal of Computational Physics, Vol. 117, Issue 1 https://doi.org/10.1006/jcph.1995.1039	journal	March 1995
Additive empirical force field for hexopyranose monosaccharides Guvench, Olgun; Greene, Shannon N.; Kamath, Ganesh Journal of Computational Chemistry, Vol. 29, Issue 15 https://doi.org/10.1002/jcc.21004	journal	November 2008
Coarse-Grain Model for Glucose, Cellobiose, and Cellotetraose in Water Hynninen, Antti-Pekka; Matthews, James F.; Beckham, Gregg T. Journal of Chemical Theory and Computation, Vol. 7, Issue 7 https://doi.org/10.1021/ct200092t	journal	June 2011
The Path Forward for Biofuels and Biomaterials Ragauskas, Arthur J.; Williams, Charlotte K.; Davison, Brian H. Science, Vol. 311, Issue 5760, p. 484-489 https://doi.org/10.1126/science.1114736	journal	January 2006
Nanostructure of cellulose microfibrils in spruce wood Fernandes, A. N.; Thomas, L. H.; Altaner, C. M. Proceedings of the National Academy of Sciences, Vol. 108, Issue 47 https://doi.org/10.1073/pnas.1108942108	journal	November 2011
OPLS all-atom force field for carbohydrates Damm, Wolfgang; Frontera, Antonio; Tirado-Rives, Julian Journal of Computational Chemistry, Vol. 18, Issue 16 https://doi.org/10.1002/(SICI)1096-987X(199712)18:16<1955::AID-JCC1>3.0.CO;2-L	journal	December 1997
Computer simulation studies of microcrystalline cellulose Iβ Matthews, James F.; Skopec, Cathy E.; Mason, Philip E. Carbohydrate Research, Vol. 341, Issue 1 https://doi.org/10.1016/j.carres.2005.09.028	journal	January 2006
Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields Matthews, James F.; Beckham, Gregg T.; Bergenstråhle-Wohlert, Malin Journal of Chemical Theory and Computation, Vol. 8, Issue 2 https://doi.org/10.1021/ct2007692	journal	January 2012
Preparing Relaxed Systems of Amorphous Polymers by Multiscale Simulation: Application to Cellulose Queyroy, Séverine; Neyertz, Sylvie; Brown, David Macromolecules, Vol. 37, Issue 19 https://doi.org/10.1021/ma035821d	journal	August 2004
The Energy Landscape for the Interaction of the Family 1 Carbohydrate-Binding Module and the Cellulose Surface is Altered by Hydrolyzed Glycosidic Bonds Bu, Lintao; Beckham, Gregg T.; Crowley, Michael F. The Journal of Physical Chemistry B, Vol. 113, Issue 31 https://doi.org/10.1021/jp904003z	journal	August 2009
Systematic survey on crystalline features of algal celluloses Koyama, Makiko; Sugiyana, Junji; Itoh, Takao Cellulose, Vol. 4, Issue 2, p. 147-160 https://doi.org/10.1023/A:1018427604670	journal	January 1997
Structure of Cellulose Microfibrils in Primary Cell Walls from Collenchyma Thomas, Lynne H.; Forsyth, V. Trevor; Šturcová, Adriana Plant Physiology, Vol. 161, Issue 1 https://doi.org/10.1104/pp.112.206359	journal	November 2012
Multiscale Coarse-Graining of Monosaccharides Liu, Pu; Izvekov, Sergei; Voth, Gregory. A. The Journal of Physical Chemistry B, Vol. 111, Issue 39 https://doi.org/10.1021/jp0721494	journal	October 2007
A Multiscale Coarse-Graining Method for Biomolecular Systems Izvekov, Sergei; Voth, Gregory A. The Journal of Physical Chemistry B, Vol. 109, Issue 7 https://doi.org/10.1021/jp044629q	journal	February 2005
Dynamics of large proteins through hierarchical levels of coarse-grained structures Doruker, Pemra; Jernigan, Robert L.; Bahar, Ivet Journal of Computational Chemistry, Vol. 23, Issue 1 https://doi.org/10.1002/jcc.1160	journal	November 2001
CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses Guvench, Olgun; Hatcher, Elizabeth; Venable, Richard M. Journal of Chemical Theory and Computation, Vol. 5, Issue 9 https://doi.org/10.1021/ct900242e	journal	August 2009
Deriving effective mesoscale potentials from atomistic simulations: Mesoscale Potentials from Atomistic Simulations Reith, Dirk; Pütz, Mathias; Müller-Plathe, Florian Journal of Computational Chemistry, Vol. 24, Issue 13 https://doi.org/10.1002/jcc.10307	journal	August 2003
Optimization of the isolation of nanocrystals from microcrystalline cellulose by acid hydrolysis Bondeson, Daniel; Mathew, Aji; Oksman, Kristiina Cellulose, Vol. 13, Issue 2 https://doi.org/10.1007/s10570-006-9061-4	journal	April 2006
The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations Marrink, Siewert J.; Risselada, H. Jelger; Yefimov, Serge The Journal of Physical Chemistry B, Vol. 111, Issue 27 https://doi.org/10.1021/jp071097f	journal	July 2007
Force Pulling of Single Cellulose Chains at the Crystalline Cellulose−Liquid Interface: A Molecular Dynamics Study Bergenstråhle, Malin; Thormann, Esben; Nordgren, Niklas Langmuir, Vol. 25, Issue 8 https://doi.org/10.1021/la803915c	journal	April 2009
Estimation of the lateral dimensions of cellulose crystallites using NMR signal strengths Newman, Roger H. Solid State Nuclear Magnetic Resonance, Vol. 15, Issue 1 https://doi.org/10.1016/S0926-2040(99)00043-0	journal	October 1999
The MARTINI Coarse-Grained Force Field: Extension to Proteins Monticelli, Luca; Kandasamy, Senthil K.; Periole, Xavier Journal of Chemical Theory and Computation, Vol. 4, Issue 5 https://doi.org/10.1021/ct700324x	journal	April 2008
Solid-State 13C NMR Investigation of Molecular Ordering in the Cellulose of Apple Cell Walls Newman, Roger H.; Ha, Marie-Ann; Melton, Laurence D. Journal of Agricultural and Food Chemistry, Vol. 42, Issue 7 https://doi.org/10.1021/jf00043a002	journal	July 1994
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems Darden, Tom; York, Darrin; Pedersen, Lee The Journal of Chemical Physics, Vol. 98, Issue 12 https://doi.org/10.1063/1.464397	journal	June 1993
Molecular weight distribution of cellulose in primary cell walls: Investigations with regenerating protoplasts, suspension cultured cells and mesophyll of tobacco Blaschek, W.; Koehler, H.; Semler, U. Planta, Vol. 154, Issue 6 https://doi.org/10.1007/BF00402999	journal	June 1982
Structural Micro-heterogeneities of Crystalline Iβ-cellulose Mazeau, Karim Cellulose, Vol. 12, Issue 4 https://doi.org/10.1007/s10570-005-2200-5	journal	August 2005
Coarse-grained models for proteins Tozzini, Valentina Current Opinion in Structural Biology, Vol. 15, Issue 2 https://doi.org/10.1016/j.sbi.2005.02.005	journal	April 2005
Comparison of simple potential functions for simulating liquid water Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D. The Journal of Chemical Physics, Vol. 79, Issue 2 https://doi.org/10.1063/1.445869	journal	July 1983
The xyloglucan–cellulose assembly at the atomic scale Hanus, Jaroslav; Mazeau, Karim Biopolymers, Vol. 82, Issue 1 https://doi.org/10.1002/bip.20460	journal	January 2006
Analysis of Twisting of Cellulose Nanofibrils in Atomistic Molecular Dynamics Simulations Paavilainen, Sami; Róg, Tomasz; Vattulainen, Ilpo The Journal of Physical Chemistry B, Vol. 115, Issue 14 https://doi.org/10.1021/jp111459b	journal	April 2011
Coarse Grained Protein−Lipid Model with Application to Lipoprotein Particles ^† Shih, Amy Y.; Arkhipov, Anton; Freddolino, Peter L. The Journal of Physical Chemistry B, Vol. 110, Issue 8 https://doi.org/10.1021/jp0550816	journal	March 2006
Determination of the leveling-off degree of polymerization of cotton and rayon Nelson, Mary L.; Tripp, Verne W. Journal of Polymer Science, Vol. 10, Issue 6 https://doi.org/10.1002/pol.1953.120100608	journal	June 1953
A Coarse-Grained Model for Molecular Dynamics Simulations of Native Cellulose Wohlert, Jakob; Berglund, Lars A. Journal of Chemical Theory and Computation, Vol. 7, Issue 3 https://doi.org/10.1021/ct100489z	journal	January 2011
Thermal Response in Crystalline Iβ Cellulose: A Molecular Dynamics Study Bergenstråhle, Malin; Berglund, Lars A.; Mazeau, Karim The Journal of Physical Chemistry B, Vol. 111, Issue 30 https://doi.org/10.1021/jp072258i	journal	August 2007
Periodic Disorder along Ramie Cellulose Microfibrils Nishiyama, Yoshiharu; Kim, Ung-Jin; Kim, Dae-Young Biomacromolecules, Vol. 4, Issue 4 https://doi.org/10.1021/bm025772x	journal	July 2003
A Revised Architecture of Primary Cell Walls Based on Biomechanical Changes Induced by Substrate-Specific Endoglucanases Park, Yong Bum; Cosgrove, Daniel J. Plant Physiology, Vol. 158, Issue 4 https://doi.org/10.1104/pp.111.192880	journal	February 2012
Coarse-grained normal mode analysis in structural biology Bahar, Ivet; Rader, Aj Current Opinion in Structural Biology, Vol. 15, Issue 5 https://doi.org/10.1016/j.sbi.2005.08.007	journal	October 2005

Similar Records

Coarse-Grained Simulation of Cellulose Iβ with Application to Long Fibrils

Journal Article · Thu Oct 30 00:00:00 EDT 2014 · Cellulose · OSTI ID:1168390

Coarse-grain model for natural cellulose fibrils in explicit water

Journal Article · Sun Feb 23 23:00:00 EST 2014 · Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry · OSTI ID:1265933

REACH coarse-grained simulation of a cellulose fiber

Journal Article · Fri Aug 31 00:00:00 EDT 2012 · Biomacromolecules · OSTI ID:1265965

Related Subjects

biofuels (including algae and biomass)
bio-inspired
membrane
carbon sequestration
materials and chemistry by design
synthesis (self-assembly)

Coarse-grained simulation of cellulose Iβ with application to long fibrils

Citation Formats

References (63)

Similar Records

Related Subjects